Genomic Characterization of a Polyvalent Hydrocarbonoclastic Bacterium Pseudomonas Sp. Strain BUN14

Total Page:16

File Type:pdf, Size:1020Kb

Genomic Characterization of a Polyvalent Hydrocarbonoclastic Bacterium Pseudomonas Sp. Strain BUN14 www.nature.com/scientificreports OPEN Genomic characterization of a polyvalent hydrocarbonoclastic bacterium Pseudomonas sp. strain BUN14 Mouna Mahjoubi1, Habibu Aliyu2, Mohamed Neifar1, Simone Cappello3, Habib Chouchane1, Yasmine Souissi1, Ahmed Salaheddine Masmoudi1, Don A. Cowan4 & Ameur Cherif1* Bioremediation ofers a viable alternative for the reduction of contaminants from the environment, particularly petroleum and its recalcitrant derivatives. In this study, the ability of a strain of Pseudomonas BUN14 to degrade crude oil, pristane and dioxin compounds, and to produce biosurfactants, was investigated. BUN14 is a halotolerant strain isolated from polluted sediment recovered from the refnery harbor on the Bizerte coast, north Tunisia and capable of producing surfactants. The strain BUN14 was assembled into 22 contigs of 4,898,053 bp with a mean GC content of 62.4%. Whole genome phylogeny and comparative genome analyses showed that strain BUN14 could be afliated with two validly described Pseudomonas Type Strains, P. kunmingensis DSM 25974T and P. chloritidismutans AW-1T. The current study, however, revealed that the two Type Strains are probably conspecifc and, given the priority of the latter, we proposed that P. kunmingensis DSM 25974 is a heteronym of P. chloritidismutans AW-1T. Using GC-FID analysis, we determined that BUN14 was able to use a range of hydrocarbons (crude oil, pristane, dibenzofuran, dibenzothiophene, naphthalene) as a sole carbon source. Genome analysis of BUN14 revealed the presence of a large repertoire of proteins (154) related to xenobiotic biodegradation and metabolism. Thus, 44 proteins were linked to the pathways for complete degradation of benzoate and naphthalene. The annotation of conserved functional domains led to the detection of putative genes encoding enzymes of the rhamnolipid biosynthesis pathway. Overall, the polyvalent hydrocarbon degradation capacity of BUN14 makes it a promising candidate for application in the bioremediation of polluted saline environments. Petroleum and dioxins compounds are omnipresent environmental pollutants that threaten the environment and human health due to their toxicological properties and their high resistance to degradation 1,2. Bioremediation is considered as one of the viable options for remediation of hydrocarbon-polluted environments 3,4. Numerous microorganisms, including bacteria, fungi, archaea and algae, have been investigated for their bioremediation potential3,4 with 79 bacterial genera reported to possess the capacity to degrade hydrocarbons 3. Members of the Gammaproteobacteria class have high hydrocarbon-degrading capacity, and this taxon includes the most obligate hydrocarbonoclastic genera: Alcanivorax, Talassolituus, Oleiphilus, Oleispira, Cycloclasticus and Mar- inobacter3,56. However, other non-obligate hydrocarbonoclastic members of the Gammaproteobacteria, such as the genus Pseudomonas, are well known for their hydrocarbon-degrading capacity 47. Te genetic basis and enzymatic mechanisms involved in the degradation of oil components, including alkanes and aromatic com- pounds, by Pseudomonas species have been reported in detail 8,9. Te key activating enzymes in the degradation of alkanes are alkane hydroxylases 10. Alkane monooxygenases (AlkB) and cytochrome P450s (CYP153) catalyze the hydroxylation of alkanes to alcohols, which are subsequently oxidized to fatty acids. Te fatty acid products are further metabolized by β-oxidation10. Te catabolism of aromatic compounds involves multiple enzymes which convert the aromatic substrates into Krebs cycle intermediates via ortho or meta-cleavage pathways. Te 1University of Manouba, ISBST, BVBGR-LR11ES31, Biotechpole SidiThabet, 2020 Ariana, Tunisia. 2Institute of Process Engineering in Life Science 2: Technical Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany. 3Istituto per le Risorse Biologiche e le Biotecnologie Marine (IRBIM)-CNR of Messina, Sp. San Raineri, 86, 98122 Messina, Italy. 4Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria 0002, South Africa. *email: [email protected] Scientifc Reports | (2021) 11:8124 | https://doi.org/10.1038/s41598-021-87487-2 1 Vol.:(0123456789) www.nature.com/scientificreports/ l3-ketoadipate pathway (ortho-cleavage pathway) is the key route for the catabolism of a wide variety of aromatic compounds through the protocatechuate branch (pea genes) and the catechol branch (cat genes). Te phylogeny of the genus Pseudomonas is complex, with some 219 validly published and correctly named species11. However, the current phylogeny is subject to considerable debate12 and many of the named species may be considered as conspecifc. For example, Pseudomonas kunmingensis HL22-2T and P. chloritidismutans AW-1T which are closely related to P. stutzeri may not deserve separate species status 13,14. To date, the genome sequences of eighteen strains afliated to P. kunmingensis and one afliated to P. chl or- itidismutans strain are available via the NCBI database 15. While the genes and pathways associated with n-alkane degradation have been reported for P. chloritidismutans16,17, similar information for Pseudomonas kunmingensis is not available. Pseudomonas sp. BUN14, isolated from hydrocarbon-polluted sediments from the Bizerte coast refnery harbour, north Tunisia, exhibits the capacity for hydrocarbon degradation. In this study, we combined genomic analysis and degradation experiments to demonstrate that Pseudomonas strain BUN14 has potential for applica- tion in the bioremediation of hydrocarbon contaminated marine environments. Results and discussion Isolation, phylogenetic assignment, and characterization of hydrocarbonoclastic bacterial strain BUN14. Strain BUN14 was isolated on ONR7a mineral medium supplemented with 1% crude oil as the sole carbon source. Te comparison of the strain BUN14 16S rRNA gene sequence with those of validly described strains in the EzBioCloud18,19 revealed that strain BUN14 showed highest similarity (99.23%) to that of P. kunmingensis HL22-2T Phylogenetic analysis based on the 16S rRNA gene of Pseudomonas species placed P. kunmingensis HL22-2T as the closest relative of BUN14 (Fig. S1). Growth of strain BUN14 on plates containing TSA (Trypticase soy agar) medium showed that the bacterium formed circular, opaque yellow colonies. Cells were rod-shaped and approximately 0.6 ± 0.1 μm in diameter and 1.8–2.0 μm in length (Fig. S2). Optimization of surfactant activities. When grown on mineral medium ONR7a supplemented with crude oil and vegetable oil as sole carbon sources, BUN14 strain produced biosurfactants, as indicated by the oil spreading, drop collapse and emulsifcation tests (Fig. S2). Use of the Cetyl Tri Ammonium Bromide (CTAB)- Methylene blue agar method indicated that BUN14 produced anionic biosurfactant (Fig. S2). Optimal condi- tions for growth and biosurfactant production were assessed using response surface methodology (RSM) experi- ments. Te analysis of variance for the ftted mathematical models shows that the regression sum of squares was statistically signifcant (P < 0.01) (Table S5). Response surface plots, showing optimal biosurfactant production conditions, are shown in Fig. 1. Statistical analyses of central composite design (CCD) experiments demon- strated that the percentage of oil substrate, NaCl concentration, inoculum size and incubation time all afected the biosurfactant production. Based on desirability function, the optimal BUN14 growth (OD 600nm, 0.54), bio- surfactant production (OD 625nm, 2.58) and activities (emulsion index E24, 40.09% and oil-displacement ODA, 20.40 cm2), were obtained afer approx. 7 days of cultivation crude oil, 2.50% NaCl concentration inoculum size source (Fig. S3). Accordingly, as for previous studies20,21 substrate, NaCl concentration, inoculum size and incu- bation time signifcantly afected biosurfactant production (0.01 < p < 0.05). Te basic structure of the isolated biosurfactant was evaluated by Fourier Transform InfraRed (FT-IR) spec- trometry and compared to a reference Pseudomonas aeruginosa (Fig. 2). Te peaks appearing at 3278.56 (Fig. 2a) and 3270.42 cm−1 (Fig. 2b) denoted the presence of –OH stretching (free hydroxyl groups of rhamnose rings) of hydroxyl group. Te adsorption peaks at 2924.64 (Fig. 2b) and 3000.0 cm−1 (Fig. 2a) indicated the presence of terminal methyl group of aliphatic stretching bands (CH2, CH3). Te absorption peaks at 1097.35 (Fig. 2a) and 1049.1 cm−1 (Fig. 2b) confrmed the presence of C–O–C vibrations (rhamnose ring). Te area between 1495.92 and 1150.02 cm−1 (Fig. 2a) represented C–H and OH deformation vibrations typical for carbohydrates, as in the rhamnose units of the biosurfactant. Te apparent similarity of the main functional groups determined by FTIR spectrometry of the commercial rhamnolipid (R90) from Pseudomonas aeruginosa (AGAE Technologies, Corval- lis, OR, USA) and the isolated biomolecule from strain BUN14 (Fig. 2), suggested that the BUN14 biosurfactant product was composed on rhamnose rings with long hydrocarbon chains. Members of the genus Pseudomonas are known for biosynthesis of rhamnolipids with biosurfactant properties20,22. Hydrocarbon degradation. Strain BUN14 could grow on and utilize various hydrocarbons, including pyrene, naphthalene, phenanthrene, carbazole, dibenzofuran, dibenzothiohene, biphenyl, pristane, fuoran- thene, crude oil, octadecane and tetradecane as sole carbon and energy sources (Fig. S4a–c). Tese fndings are in agreement with previous reports demonstrating that
Recommended publications
  • Deep Microbial Community Profiling Along the Fermentation Process of Pulque, a Major Biocultural Resource of Mexico
    bioRxiv preprint doi: https://doi.org/10.1101/718999; this version posted July 31, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Deep microbial community profiling along the fermentation process of pulque, a major biocultural resource of Mexico. 1 1 2 Carolina Rocha-Arriaga ,​ Annie Espinal-Centeno ,​ Shamayim Martinez-Sanchez ,​ Juan ​ ​ 1 2 ​ 1,3 ​ Caballero-Pérez ,​ Luis D. Alcaraz *​ & Alfredo Cruz-Ramirez *.​ ​ ​ ​ 1 Molecular​ & Developmental Complexity Group, Unit of Advanced Genomics, LANGEBIO-CINVESTAV, Irapuato, México. 2 Laboratorio​ de Genómica Ambiental, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México. Cd. Universitaria, 04510 Coyoacán, Mexico City, Mexico. 3 Escuela​ de Agronomía, Universidad de La Salle Bajío, León, Gto, Mexico. *Corresponding authors: [email protected], [email protected] ​ ​ ​ ● ​Our approach allowed the identification of a broader microbial diversity in Pulque ● We increased 4.4 times bacteria genera and 40 times fungal species detected in mead. ● Newly reported bacteria genera and fungal species associated to Pulque fermentation Abstract Some of the biggest non-three plants endemic to Mexico were called metl in the Nahua culture. ​ During colonial times they were renamed with the antillan word maguey. This was changed ​ ​ again by Carl von Linné who called them Agave (a greco-latin voice for admirable). For several ​ Mexican prehispanic cultures, Agave species were not only considered as crops, but also part ​ of their biocultural resources and cosmovision. Among the major products obtained from some Agave spp since pre-hispanic times is the alcoholic beverage called pulque or octli.
    [Show full text]
  • Doctoral Thesis 2016 UNDERSTANDING the AROMATIC HYDROCARBON DEGRADATION POTENTIAL of PSEUDOMONAS STUTZERI
    Doctoral Thesis 2016 UNDERSTANDING THE AROMATIC HYDROCARBON DEGRADATION POTENTIAL OF PSEUDOMONAS STUTZERI: A PROTEO-GENOMIC APPROACH Isabel Brunet Galmés Doctoral Thesis 2016 Doctoral Program of “Microbiologia Ambiental i Biotecnologia” UNDERSTANDING THE AROMATIC HYDROCARBON DEGRADATION POTENTIAL OF PSEUDOMONAS STUTZERI: A PROTEO-GENOMIC APPROACH Isabel Brunet Galmés Thesis Supervisor: Dr. Rafael Bosch Thesis Supervisor: Dra. Balbina Nogales Doctor by the Universitat de les Illes Balears A mumpare i a mumare Agraïments Gràcies Rafel i Balbina per dirigir aquesta tesis, que és tant meva com vostre. A en Rafel per l’oportunitat que em vares donar, ja fa 7 anys, d’entrar al laboratori. Així com també per engrescar-me dins el món de la ciència, i ensenyar-me a treballar tant dins com fora del laboratori. I a na Balbina, pels mil consells que m’ha donat aquests anys, per ensenyar-me a ser més meticulosa amb el que faig i per ajudar-me amb tot el que ha pogut. A en Jordi i n’Elena, per acollir-me dins aquest grup de recerca, pels vostres consells i noves idees per continuar aquesta feina. Voldria agrair també a en Toni Bennasar i en Sebastià les crítiques constructives que m’heu anat fent al llarg d’aquests anys, des del projecte final de màster fins ara. Gràcies també a tots els companys de laboratori, a més de companys sou uns grans amics. Sempre estaré agraïda a na Marga, en Toni Busquets i n’Arantxa, pels grans consells que m’heu donat, tant dins com fora del laboratori, i per estar sempre disposats a donar-me una mà.
    [Show full text]
  • Tesis Doctoral 2014 Filogenia Y Evolución De Las Poblaciones Ambientales Y Clínicas De Pseudomonas Stutzeri Y Otras Especies
    TESIS DOCTORAL 2014 FILOGENIA Y EVOLUCIÓN DE LAS POBLACIONES AMBIENTALES Y CLÍNICAS DE PSEUDOMONAS STUTZERI Y OTRAS ESPECIES RELACIONADAS Claudia A. Scotta Botta TESIS DOCTORAL 2014 Programa de Doctorado de Microbiología Ambiental y Biotecnología FILOGENIA Y EVOLUCIÓN DE LAS POBLACIONES AMBIENTALES Y CLÍNICAS DE PSEUDOMONAS STUTZERI Y OTRAS ESPECIES RELACIONADAS Claudia A. Scotta Botta Director/a: Jorge Lalucat Jo Director/a: Margarita Gomila Ribas Director/a: Antonio Bennasar Figueras Doctor/a por la Universitat de les Illes Balears Index Index ……………………………………………………………………………..... 5 Acknowledgments ………………………………………………………………... 7 Abstract/Resumen/Resum ……………………………………………………….. 9 Introduction ………………………………………………………………………. 15 I.1. The genus Pseudomonas ………………………………………………….. 17 I.2. The species P. stutzeri ………………………………………………......... 23 I.2.1. Definition of the species …………………………………………… 23 I.2.2. Phenotypic properties ………………………………………………. 23 I.2.3. Genomic characterization and phylogeny ………………………….. 24 I.2.4. Polyphasic identification …………………………………………… 25 I.2.5. Natural transformation ……………………………………………... 26 I.2.6. Pathogenicity and antibiotic resistance …………………………….. 26 I.3. Habitats and ecological relevance ………………………………………… 28 I.3.1. Role of mobile genetic elements …………………………………… 28 I.4. Methods for studying Pseudomonas taxonomy …………………………... 29 I.4.1. Biochemical test-based identification ……………………………… 30 I.4.2. Gas Chromatography of Cellular Fatty Acids ................................ 32 I.4.3. Matrix Assisted Laser-Desorption Ionization Time-Of-Flight
    [Show full text]
  • CUED Phd and Mphil Thesis Classes
    High-throughput Experimental and Computational Studies of Bacterial Evolution Lars Barquist Queens' College University of Cambridge A thesis submitted for the degree of Doctor of Philosophy 23 August 2013 Arrakis teaches the attitude of the knife { chopping off what's incomplete and saying: \Now it's complete because it's ended here." Collected Sayings of Muad'dib Declaration High-throughput Experimental and Computational Studies of Bacterial Evolution The work presented in this dissertation was carried out at the Wellcome Trust Sanger Institute between October 2009 and August 2013. This dissertation is the result of my own work and includes nothing which is the outcome of work done in collaboration except where specifically indicated in the text. This dissertation does not exceed the limit of 60,000 words as specified by the Faculty of Biology Degree Committee. This dissertation has been typeset in 12pt Computer Modern font using LATEX according to the specifications set by the Board of Graduate Studies and the Faculty of Biology Degree Committee. No part of this dissertation or anything substantially similar has been or is being submitted for any other qualification at any other university. Acknowledgements I have been tremendously fortunate to spend the past four years on the Wellcome Trust Genome Campus at the Sanger Institute and the European Bioinformatics Institute. I would like to thank foremost my main collaborators on the studies described in this thesis: Paul Gardner and Gemma Langridge. Their contributions and support have been invaluable. I would also like to thank my supervisor, Alex Bateman, for giving me the freedom to pursue a wide range of projects during my time in his group and for advice.
    [Show full text]
  • Comparative Genomic Analysis of Three Pseudomonas
    microorganisms Article Comparative Genomic Analysis of Three Pseudomonas Species Isolated from the Eastern Oyster (Crassostrea virginica) Tissues, Mantle Fluid, and the Overlying Estuarine Water Column Ashish Pathak 1, Paul Stothard 2 and Ashvini Chauhan 1,* 1 Environmental Biotechnology Laboratory, School of the Environment, 1515 S. Martin Luther King Jr. Blvd., Suite 305B, FSH Science Research Center, Florida A&M University, Tallahassee, FL 32307, USA; [email protected] 2 Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G2P5, Canada; [email protected] * Correspondence: [email protected]; Tel.: +1-850-412-5119; Fax: +1-850-561-2248 Abstract: The eastern oysters serve as important keystone species in the United States, especially in the Gulf of Mexico estuarine waters, and at the same time, provide unparalleled economic, ecological, environmental, and cultural services. One ecosystem service that has garnered recent attention is the ability of oysters to sequester impurities and nutrients, such as nitrogen (N), from the estuarine water that feeds them, via their exceptional filtration mechanism coupled with microbially-mediated denitrification processes. It is the oyster-associated microbiomes that essentially provide these myriads of ecological functions, yet not much is known on these microbiota at the genomic scale, especially from warm temperate and tropical water habitats. Among the suite of bacterial genera that appear to interplay with the oyster host species, pseudomonads deserve further assessment because Citation: Pathak, A.; Stothard, P.; of their immense metabolic and ecological potential. To obtain a comprehensive understanding on Chauhan, A. Comparative Genomic this aspect, we previously reported on the isolation and preliminary genomic characterization of Analysis of Three Pseudomonas Species three Pseudomonas species isolated from minced oyster tissue (P.
    [Show full text]
  • Pseudomonas Chloritidismutans Sp. Nov., a Non- Denitrifying, Chlorate-Reducing Bacterium
    International Journal of Systematic and Evolutionary Microbiology (2002), 52, 2183–2190 DOI: 10.1099/ijs.0.02102-0 Pseudomonas chloritidismutans sp. nov., a non- denitrifying, chlorate-reducing bacterium Laboratory of Microbiology, A. F. W. M. Wolterink, A. B. Jonker, S. W. M. Kengen and A. J. M. Stams Wageningen University, H. van Suchtelenweg 4, 6703 CT Wageningen, Author for correspondence: The Netherlands A. F. W. M. Wolterink. Tel: j31 317 484099. Fax: j31 317 483829. e-mail: Arthur.Wolterink!algemeen.micr.wag-ur.nl A Gram-negative, facultatively anaerobic, rod-shaped, dissimilatory chlorate- reducing bacterium, strain AW-1T, was isolated from biomass of an anaerobic chlorate-reducing bioreactor. Phylogenetic analysis of the 16S rDNA sequence showed 100% sequence similarity to Pseudomonas stutzeri DSM 50227 and 986% sequence similarity to the type strain of P. stutzeri (DSM 5190T). The species P. stutzeri possesses a high degree of genotypic and phenotypic heterogeneity. Therefore, eight genomic groups, termed genomovars, have been proposed based upon ∆Tm values, which were used to evaluate the quality of the pairing within heteroduplexes formed by DNA–DNA hybridization. In this study, DNA–DNA hybridization between strain AW-1T and P. stutzeri strains DSM 50227 and DSM 5190T revealed respectively 805 and 565% similarity. DNA–DNA hybridization between P. stutzeri strains DSM 50227 and DSM 5190T revealed 484% similarity. DNA–DNA hybridization indicated that strain AW-1T is not related at the species level to the type strain of P. stutzeri. However, strain AW-1T and P. stutzeri DSM 50227 are related at the species level. The physiological and biochemical properties of strain AW-1T and the two P.
    [Show full text]
  • Table S5. the Information of the Bacteria Annotated in the Soil Community at Species Level
    Table S5. The information of the bacteria annotated in the soil community at species level No. Phylum Class Order Family Genus Species The number of contigs Abundance(%) 1 Firmicutes Bacilli Bacillales Bacillaceae Bacillus Bacillus cereus 1749 5.145782459 2 Bacteroidetes Cytophagia Cytophagales Hymenobacteraceae Hymenobacter Hymenobacter sedentarius 1538 4.52499338 3 Gemmatimonadetes Gemmatimonadetes Gemmatimonadales Gemmatimonadaceae Gemmatirosa Gemmatirosa kalamazoonesis 1020 3.000970902 4 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas indica 797 2.344876284 5 Firmicutes Bacilli Lactobacillales Streptococcaceae Lactococcus Lactococcus piscium 542 1.594633558 6 Actinobacteria Thermoleophilia Solirubrobacterales Conexibacteraceae Conexibacter Conexibacter woesei 471 1.385742446 7 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas taxi 430 1.265115184 8 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas wittichii 388 1.141545794 9 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas sp. FARSPH 298 0.876754244 10 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sorangium cellulosum 260 0.764953367 11 Proteobacteria Deltaproteobacteria Myxococcales Polyangiaceae Sorangium Sphingomonas sp. Cra20 260 0.764953367 12 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas panacis 252 0.741416341
    [Show full text]
  • Understanding the Composition and Role of the Prokaryotic Diversity in the Potato Rhizosphere for Crop Improvement in the Andes
    Understanding the composition and role of the prokaryotic diversity in the potato rhizosphere for crop improvement in the Andes Jonas Ghyselinck Dissertation submitted in fulfilment of the requirements for the degree of Doctor (Ph.D.) in Sciences, Biotechnology Promotor - Prof. Dr. Paul De Vos Co-promotor - Dr. Kim Heylen Ghyselinck Jonas – Understanding the composition and role of the prokaryotic diversity in the potato rhizosphere for crop improvement in the Andes Copyright ©2013 Ghyselinck Jonas ISBN-number: 978-94-6197-119-7 No part of this thesis protected by its copyright notice may be reproduced or utilized in any form, or by any means, electronic or mechanical, including photocopying, recording or by any information storage or retrieval system without written permission of the author and promotors. Printed by University Press | www.universitypress.be Ph.D. thesis, Faculty of Sciences, Ghent University, Ghent, Belgium. This Ph.D. work was financially supported by European Community's Seventh Framework Programme FP7/2007-2013 under grant agreement N° 227522 Publicly defended in Ghent, Belgium, May 28th 2013 EXAMINATION COMMITTEE Prof. Dr. Savvas Savvides (chairman) Faculty of Sciences Ghent University, Belgium Prof. Dr. Paul De Vos (promotor) Faculty of Sciences Ghent University, Belgium Dr. Kim Heylen (co-promotor) Faculty of Sciences Ghent University, Belgium Prof. Dr. Anne Willems Faculty of Sciences Ghent University, Belgium Prof. Dr. Peter Dawyndt Faculty of Sciences Ghent University, Belgium Prof. Dr. Stéphane Declerck Faculty of Biological, Agricultural and Environmental Engineering Université catholique de Louvain, Louvain-la-Neuve, Belgium Dr. Angela Sessitsch Department of Health and Environment, Bioresources Unit AIT Austrian Institute of Technology GmbH, Tulln, Austria Dr.
    [Show full text]
  • (Antarctica) Glacial, Basal, and Accretion Ice
    CHARACTERIZATION OF ORGANISMS IN VOSTOK (ANTARCTICA) GLACIAL, BASAL, AND ACCRETION ICE Colby J. Gura A Thesis Submitted to the Graduate College of Bowling Green State University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE December 2019 Committee: Scott O. Rogers, Advisor Helen Michaels Paul Morris © 2019 Colby Gura All Rights Reserved iii ABSTRACT Scott O. Rogers, Advisor Chapter 1: Lake Vostok is named for the nearby Vostok Station located at 78°28’S, 106°48’E and at an elevation of 3,488 m. The lake is covered by a glacier that is approximately 4 km thick and comprised of 4 different types of ice: meteoric, basal, type 1 accretion ice, and type 2 accretion ice. Six samples were derived from the glacial, basal, and accretion ice of the 5G ice core (depths of 2,149 m; 3,501 m; 3,520 m; 3,540 m; 3,569 m; and 3,585 m) and prepared through several processes. The RNA and DNA were extracted from ultracentrifugally concentrated meltwater samples. From the extracted RNA, cDNA was synthesized so the samples could be further manipulated. Both the cDNA and the DNA were amplified through polymerase chain reaction. Ion Torrent primers were attached to the DNA and cDNA and then prepared to be sequenced. Following sequencing the sequences were analyzed using BLAST. Python and Biopython were then used to collect more data and organize the data for manual curation and analysis. Chapter 2: As a result of the glacier and its geographic location, Lake Vostok is an extreme and unique environment that is often compared to Jupiter’s ice-covered moon, Europa.
    [Show full text]
  • Étude Des Communautés Microbiennes Rhizosphériques De Ligneux Indigènes De Sols Anthropogéniques, Issus D’Effluents Industriels Cyril Zappelini
    Étude des communautés microbiennes rhizosphériques de ligneux indigènes de sols anthropogéniques, issus d’effluents industriels Cyril Zappelini To cite this version: Cyril Zappelini. Étude des communautés microbiennes rhizosphériques de ligneux indigènes de sols anthropogéniques, issus d’effluents industriels. Sciences agricoles. Université Bourgogne Franche- Comté, 2018. Français. NNT : 2018UBFCD057. tel-01902775 HAL Id: tel-01902775 https://tel.archives-ouvertes.fr/tel-01902775 Submitted on 23 Oct 2018 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. UNIVERSITÉ DE BOURGOGNE FRANCHE-COMTÉ École doctorale Environnement-Santé Laboratoire Chrono-Environnement (UMR UFC/CNRS 6249) THÈSE Présentée en vue de l’obtention du titre de Docteur de l’Université Bourgogne Franche-Comté Spécialité « Sciences de la Vie et de l’Environnement » ÉTUDE DES COMMUNAUTES MICROBIENNES RHIZOSPHERIQUES DE LIGNEUX INDIGENES DE SOLS ANTHROPOGENIQUES, ISSUS D’EFFLUENTS INDUSTRIELS Présentée et soutenue publiquement par Cyril ZAPPELINI Le 3 juillet 2018, devant le jury composé de : Membres du jury : Vera SLAVEYKOVA (Professeure, Univ. de Genève) Rapporteure Bertrand AIGLE (Professeur, Univ. de Lorraine) Rapporteur & président du jury Céline ROOSE-AMSALEG (IGR, Univ. de Rennes) Examinatrice Karine JEZEQUEL (Maître de conférences, Univ. de Haute Alsace) Examinatrice Nicolas CAPELLI (Maître de conférences HDR, UBFC) Encadrant Christophe GUYEUX (Professeur, UBFC) Co-directeur de thèse Michel CHALOT (Professeur, UBFC) Directeur de thèse « En vérité, le chemin importe peu, la volonté d'arriver suffit à tout.
    [Show full text]
  • Evolutionary Genomics of an Ancient Prophage of the Order Sphingomonadales
    GBE Evolutionary Genomics of an Ancient Prophage of the Order Sphingomonadales Vandana Viswanathan1,2, Anushree Narjala1, Aravind Ravichandran1, Suvratha Jayaprasad1,and Shivakumara Siddaramappa1,* 1Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronic City, Bengaluru, Karnataka, India 2Manipal University, Manipal, Karnataka, India *Corresponding author: E-mail: [email protected]. Accepted: February 10, 2017 Data deposition: Genome sequences were downloaded from GenBank, and their accession numbers are provided in table 1. Abstract The order Sphingomonadales, containing the families Erythrobacteraceae and Sphingomonadaceae, is a relatively less well-studied phylogenetic branch within the class Alphaproteobacteria. Prophage elements are present in most bacterial genomes and are important determinants of adaptive evolution. An “intact” prophage was predicted within the genome of Sphingomonas hengshuiensis strain WHSC-8 and was designated Prophage IWHSC-8. Loci homologous to the region containing the first 22 open reading frames (ORFs) of Prophage IWHSC-8 were discovered among the genomes of numerous Sphingomonadales.In17genomes, the homologous loci were co-located with an ORF encoding a putative superoxide dismutase. Several other lines of molecular evidence implied that these homologous loci represent an ancient temperate bacteriophage integration, and this horizontal transfer event pre-dated niche-based speciation within the order Sphingomonadales. The “stabilization” of prophages in the genomes of their hosts is an indicator of “fitness” conferred by these elements and natural selection. Among the various ORFs predicted within the conserved prophages, an ORF encoding a putative proline-rich outer membrane protein A was consistently present among the genomes of many Sphingomonadales. Furthermore, the conserved prophages in six Sphingomonas sp. contained an ORF encoding a putative spermidine synthase.
    [Show full text]
  • Pseudomonas Stutzeri Biology Of
    Biology of Pseudomonas stutzeri Jorge Lalucat, Antoni Bennasar, Rafael Bosch, Elena García-Valdés and Norberto J. Palleroni Microbiol. Mol. Biol. Rev. 2006, 70(2):510. DOI: 10.1128/MMBR.00047-05. Downloaded from Updated information and services can be found at: http://mmbr.asm.org/content/70/2/510 These include: http://mmbr.asm.org/ REFERENCES This article cites 395 articles, 145 of which can be accessed free at: http://mmbr.asm.org/content/70/2/510#ref-list-1 CONTENT ALERTS Receive: RSS Feeds, eTOCs, free email alerts (when new articles cite this article), more» on January 28, 2014 by Red de Bibliotecas del CSIC Information about commercial reprint orders: http://journals.asm.org/site/misc/reprints.xhtml To subscribe to to another ASM Journal go to: http://journals.asm.org/site/subscriptions/ MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS, June 2006, p. 510–547 Vol. 70, No. 2 1092-2172/06/$08.00ϩ0 doi:10.1128/MMBR.00047-05 Copyright © 2006, American Society for Microbiology. All Rights Reserved. Biology of Pseudomonas stutzeri Jorge Lalucat,1,2* Antoni Bennasar,1 Rafael Bosch,1 Elena Garcı´a-Valde´s,1,2 and Norberto J. Palleroni3 Departament de Biologia, Microbiologia, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain1; Institut Mediterrani d’Estudis Avanc¸ats (CSIC-UIB), Campus UIB, 07122 Palma de Mallorca, Spain2; and Department of Biochemistry and Microbiology, Rutgers University, Cook Campus, 3 New Brunswick, New Jersey 08901-8520 Downloaded from INTRODUCTION .......................................................................................................................................................511
    [Show full text]